The owner of Preventive Medicine Associates Inc., whose office in Vineyard Haven closed last month, pleaded not guilty yesterday to all charges alleging he engaged in a kickback scheme that fraudulently billed MassHealth nearly $3.8 million.

Dr. Punyamurtula Kishore, 61, of Brookline, was originally arrested Sept. 21 on one charge that alleged a $500,000 kickback scheme, according to Attorney General Martha Coakley’s office. But a Suffolk County indictment made public last Friday alleged a much larger scheme and listed eight counts of Medicaid kickbacks and eight of Medicaid false claims against both Dr. Kishore and his company.

He owns and manages a string of 29 medical offices in Massachusetts that provided outpatient drug and alcohol treatment to patients. The kickback scheme was aimed to induce “sober” house owners to require their residents to submit to urine drug screens performed by PMA’s labs a minimum of three times a week, said Ms. Coakley’s office.

During an arraignment Thursday in Suffolk County Superior Court, Dr. Kishore’s bail was set at $150,000 cash, according to Grant Woodman, a spokesman for the attorney general. He had been wearing a GPS monitoring device.

No Islanders have been charged in connection with the case. Last week’s indictment did name three men who are owners or managers of sober homes in Wareham, New Bedford, Sandwich, Malden and Dorchester. “The investigation is ongoing,” said Mr. Woodman.